Hepatitis C virus (HCV) is an important human pathogen that is strongly associated with transfusion related non-A, non-B (NANB) hepatitis. Patient H is a patient who has been a chronic HCV carrier for the past 13 years. We compared the nucleotide and predicted amino acid sequences of the HCV genome obtained from plasma collected in 1977 with that collected in 1990 and found that the two HCV isolates differ at 123 of the 4,923 (2.50%) nucleotides sequenced. We estimate that the mutation rate of the H strain of HCV is approximately 1.9 x 10-(3) base substitutions per genome site per year. The nucleotide changes were exclusively base substitutions and were unevenly distributed throughout the genome with a relatively high rate of change observed in the nonstructural protein number 1-like gene region. Our results suggest that the mutation rate of the HCV genome is similar to that of other RNA viruses and that HCV genes appear to be evolving at different rates within the virus genome. Although the development of a serologic assay to detect antibody to HCV has greatly extended our knowledge of NANB hepatitis, little is known about the course of viremia during HCV infection. Therefore, we investigated the pattern of serum HCV RNA using the polymerase chain reaction assay and its relationship to antibody response and clinical outcome in the course of NANB hepatitis. Serum HCV RNA first appeared within 1 week post- infection in the majority of patients examined preceding the clinical onset of hepatitis and antibody seroconversion. Viremia was transient, lasting only a few months in acute self-limited hepatitis, but persisted up to 14 years in patients chronically infected. Serum HCV RNA may provide prognostic information regarding progression of acute to chronic virus infection.